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comparison DESeq_results.xml @ 0:6f94b4b9de44 draft

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author mingchen0919
date Tue, 27 Feb 2018 23:57:53 -0500
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1 <tool id="deseq_results" name="DESeq2: Results" version="2.0.1">
2 <requirements>
3 <requirement type="package" version="1.15.0.6-0">pandoc</requirement>
4 <requirement type="package" version="1.20.0">r-getopt</requirement>
5 <requirement type="package" version="1.6">r-rmarkdown</requirement>
6 <requirement type="package" version="1.14.1">bioconductor-deseq2</requirement>
7 <requirement type="package" version="0.2">r-dt</requirement>
8 <requirement type="package" version="1.0.8">r-pheatmap</requirement>
9 </requirements>
10 <description>
11 display DESeq2 analysis results.
12 </description>
13 <stdio>
14 <!--redirecting stderr to a file. "XXX" is used to match with nothing so that tool running won't be interrupted during testing-->
15 <regex match="XXX"
16 source="stderr"
17 level="warning"
18 description="Check the warnings_and_errors.txt file for more details."/>
19 </stdio>
20 <command>
21 <![CDATA[
22
23 Rscript '${__tool_directory__}/DESeq_results_render.R'
24
25 -e $echo
26 -o $report
27 -d $report.files_path
28 -s $sink_message
29 -t '${__tool_directory__}'
30
31 ## 1. input data
32
33 -W $deseq_workspace
34 -C '$contrast_factor'
35 -T '$treatment'
36 -K '$condition'
37
38 -M '$clustering_factors'
39
40 ## 2. output report and report site directory
41 -R $deseq_results
42
43
44 ]]>
45 </command>
46 <inputs>
47 <param type="boolean" name="echo" truevalue="TRUE" falsevalue="FALSE" checked="false"
48 label="Display analysis code in report?"/>
49 <param type="data" name="deseq_workspace" format="rdata" multiple="false" optional="false"
50 label="Workspace from tool DESeq2: DESeq"/>
51 <param type="text" name="contrast_factor" label="Factor" optional="false"
52 help="the name of a factor in the design formula"/>
53 <param type="text" name="treatment" label="Treatment level" optional="false"
54 help=" the name of the numerator level for the fold change"/>
55 <param type="text" name="condition" label="Condition level" optional="false"
56 help=" the name of the denominator level for the fold change"/>
57 <param type="text" name="clustering_factors" title="Gene clustering factors" optional="false"
58 label="factors of interest for clustering samples and PCA plot"
59 help="A single factor or multiple factors from the design formula. Multiple factors are separated by comma (,)."/>
60 </inputs>
61 <outputs>
62 <data format="html" name="report" label="DESeq results report on ${on_string}" />
63 <data format="txt" name="sink_message" label="Warnings and Errors" from_work_dir="warnings_and_errors.txt"/>
64 <data format="csv" name="deseq_results" label="DESeq results on ${on_string}" from_work_dir="deseq_results.csv" />
65 </outputs>
66 <citations>
67 <citation type="bibtex">
68 @article{love2014moderated,
69 title={Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2},
70 author={Love, Michael I and Huber, Wolfgang and Anders, Simon},
71 journal={Genome biology},
72 volume={15},
73 number={12},
74 pages={550},
75 year={2014},
76 publisher={BioMed Central}
77 }
78 </citation>
79 <citation type="bibtex">
80 @article{allaire2016rmarkdown,
81 title={rmarkdown: Dynamic Documents for R, 2016},
82 author={Allaire, J and Cheng, Joe and Xie, Yihui and McPherson, Jonathan and Chang, Winston and Allen, Jeff
83 and Wickham, Hadley and Atkins, Aron and Hyndman, Rob},
84 journal={R package version 0.9},
85 volume={6},
86 year={2016}
87 }
88 </citation>
89 <citation type="bibtex">
90 @book{xie2015dynamic,
91 title={Dynamic Documents with R and knitr},
92 author={Xie, Yihui},
93 volume={29},
94 year={2015},
95 publisher={CRC Press}
96 }
97 </citation>
98 </citations>
99 </tool>